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Series GSE61238 Query DataSets for GSE61238
Status Public on Sep 10, 2014
Title Tranposable elements modulate human mRNAs and lncRNAs via specific RNA-protein interactions.
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Transposable elements (TEs) have significantly influenced the evolution of transcriptional regulatory networks in the human genome. Post-transcriptional regulation of human genes by TE-derived sequences has been observed in specific contexts, but has yet to be systematically and comprehensively investigated. Here, studied a collection of CLIP-Seq (CrossLinked ImmunoPrecipitation) experiments mapping the RNA binding sites for a diverse set of 46 human proteins across 68 experiments to explore the role of TEs in post-transcriptional regulation genome-wide via RNA-protein interactions. We detected widespread interactions between RNA binding proteins (RBPs) and various families of TE-derived sequence in the CLIP-Seq data. Alignment coverage clustered on specific positions of the TE consensus sequences, illuminating a diversity of TE-specific motifs for many RBPs. Evidence of binding and conservation of these motifs in the nonrepetitive transcriptome suggest that TEs have appropriated existing sequence preferences of the RBP. Upon depletion of the RBPs, transcripts possessing TE-derived binding sites were similarly regulated as those bound in nonrepetitive sequence. However, in a few cases the effect of RBP binding depended on the specific TE family bound—e.g., the ubiquitously expressed RBP HuR conferred opposite effects on stability to transcripts when bound to Alu elements versus other families. Our meta-analysis suggests a widespread role for TEs in shaping RNA-protein regulatory networks in the human genome.
Overall design HuR formaldehyde RIP-Seq in K562 cells, with RIP and input sequenced in triplicate.
Contributor(s) Kelley DR, Rinn JL
Citation(s) 25572935
Submission date Sep 09, 2014
Last update date May 15, 2019
Contact name David R Kelley
Phone 732-859-4305
Organization name Harvard University
Lab John Rinn
Street address 7 Divinity Ave.
City Cambridge
State/province MA
ZIP/Postal code 02138
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (6)
GSM1500072 HuR fRIP rep1
GSM1500073 HuR fRIP rep2
GSM1500074 HuR fRIP rep3
BioProject PRJNA260576
SRA SRP046700

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE61238_gene_exp.diff.gz 1.7 Mb (ftp)(http) DIFF
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Raw data are available in SRA
Processed data are available on Series record

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